I would like to lead off with a few important thank yous. First, to those who came before us, like Kincard, thank you. Second, those who research and test the mechanics of the world we call Vanadiel, Hotsoups and Bahadir, thank you. Third, and finally, anyone who contributes through discussion, thank you. And to everyone else I've not named, you can be sure you have contributed somehow to the culmination of this guide.

Comment on Playstyles

Before you tell me that it's your 12.95 and you're allowed to play how you want, know that I won't argue. Should you find that your playstyle is vastly different from mine you may not receive much insight from this guide. The information on abilities and gearsets contained within are that of an attentive player wishing to mix/max their capacity within FFXI.

Intention of this Guide

The prime intention of this guide is to outline the tools this job has available. To keep up to date on available gearsets. As well as to encourage this authors style of play. Should you find gaps of information missing, I hope I have done my part in giving you the tools to deduce the answers.

Resources

For those of you new to FFXI, welcome. Let me be the first to say that Ninja is the best job in the entirety of FFXI. With that out of the way, let's get down to bringing you up to speed.
There is a wealth of online resources available to you including this one (ffxiah.com). The first I wish to point out is the Returning to Vana'diel article on BG-Wiki.

This article covers your characters trek from level 1 to the current iLvl world of today.

Gearsets and Considerations

While there are many levels other than level 99, this guide focuses on level 99. You won't see this more than within the Equipment section. Don't worry, as I will include gearsets for those of you who may be returning or may be fresh 99's.

Each equipset shown will have 3 grades presented. I have arbitrarily chosen these 3 grades based on access to end-game events and gear.

The first grade should be accessible by anyone with minimal effort.

The second grade should be accessible by anyone with the ability to clear some Escha content and moderate RoV completion.

The third grade is designed with no limitations present. All gear is considered.

Job Traits

I'm going to save some space here and instead of covering every single passive job trait a Ninja has, I'm going to focus on the most important one:

Dual Wield
Dual wield is a progressive trait that increases the reduction of our combined weapon delay. If that sounds confusing, it is. Starting at level 10, you are able to wield two weapons, one in each hand. Your delay between attack rounds is then based off of both weapons delay added together. The very first tier of this trait we get at level 10, then further reduces this combined delay by 10%.

So we attack faster, fantastic! What's the drawback? I'm so happy you asked. The drawback is that our TP gained is also lowered from the lower delay. This isn't too terribly large of a drawback but it can have a negative effect on our TP gain if we're overloading on Dual Wield and haste at the same time.

So Langly, how much Dual Wield do I need? To answer that I need to first state that level 99 Ninjas get a total of 35% Dual Weild. If you wish to calculate how much more Dual Wield in gear is necessary with your amount of Haste you can use this formula:

One stance is perfectly suited to holding hate and the other better suited for dealing damage while going unnoticed. Do note both of these have a positioning requirement. The abilities will do nothing if the positioning requirement is not met.

You will gain many spells throughout the leveling process. Some more useful than others of course. They will fall between two types of spells. Offensive ninjutsu, which is cast on a target to either deal elemental damage or debuff the target. Or Defensive ninjutsu, which is cast on yourself to better protect against enemy attacks, buff tp gain, or alter your enmity totals. If you are returning to the game, you may not be aware of the universal tools that you can buy at Port Bastok’s Galvin’s Travel Gear Shop, or the Curio Moogle Vendors:

The names of these tools are in reference to the old Japanese card game, Hanafuda. In one form of the game, the player that ends with the Pig(猪), Deer(鹿), and Butterfly(蝶)cards of the set is declared the winner.

Offensive Ninjutsu

遁の術 -Ton

Learned at: 15 (Ichi), 40 (Ni), 99 (San)Merit

Ninja's magical nukes. Each nuke will deal corresponding elemental damage and reduce the target's resistance to another element.
See ~this thread~ for more information on ninjutsu damage calculations.

暗闇の術 Kurayami

Learned at: 19 (Ichi), 44 (Ni)

Blind effect -20Acc(Ichi) and -30Acc(Ni).

捕縄の術 Hojo

Learned at: 23 (Ichi), 48 (Ni)

Slow effect of 15%(Ichi) and 20%(Ni). Stacks with Elegy but conflicts with white magical slow.

毒盛の術 Dokumori

Learned at: 27 (Ichi)

• Usable only when you wish there was a taunt button in FFXI

呪縛の術 Jubaku

Learned at: 30 (Ichi)

Paralyze effect on target.

幽林の術 Yurin

Learned at: 83 (Ichi)
Reduces enemy TP gain.

Inhibits enemy TP gain by 10%. This effect is separate from Subtle Blow.

哀車の術 Aisha

Learned at: 78 (Ichi)

Weakens enemy attack by 15%.

Defensive Ninjutsu

空蝉の術 Utsusemi "Empty Cicada"

Learned at: 12 (Ichi), 37 (Ni), 99 (San)JP

Creates shadow images that each absorb a single attack directed at you. With the gear shown below, you can reach a maximum of 7 shadows after casting the San tier spell.

Grants the caster Subtle Blow +10. This is affected by the 50 Subtle Blow cap.

身替の術 Migawari

Learned at: 88 (Ichi)
Makes you immune from a single severely damaging attack.

Negates almost any attack that would take greater than a certain percentage of your maximum HP, and then wears off.
The more gear you wear with Migawari +, the lower the threshold for negating damage.
Capped Ninjutsu skill alone (417) pushes the threshold to 73% of your HP.

Subjob Options

When choosing a support job for your Ninja you'll need to consider a few key points. You may need to ask yourself, do I need provoke? flash? stun? or do I just need a free sneak and invis...

Warrior
Warrior is still the mainstay sub if you want to do damage. Berserk is simply one of the strongest DPS buffs in the game and while Last Resort does basically the same thing, WAR also has Agressor and Double Attack traits. It also has a convenient volatile hate spike in the form of provoke.

Rune Fencer
RUN's a very interesting sub and a lot of fun to play, giving a bit of everything. Its melee DPS actually comes very close to WAR's damage assuming you're not using Berserk (or you're attack capped anyway), which is often the case if you want to avoid the huge defense dip it does, and this is without considering lunges or resistant enemies. It also covers a lot of Ninja's weak spots, adding magic defense and evasion, as well as very reliable (at least compared to your awful -ton spells) elemental damage if you're fighting something resistant. Regen, Inquartata and Swordplay synergize with NIN's natural abilities very well. Runes also provide a small enmity boost, not nearly as much as Provoke but it does give a lot more cumulative enmity (80/320). The biggest downside is that it lacks any form of natural refresh to help with that small MP pool- remember to take a couple juices. Having Flash at the ready will keep hate focused on you and give you a small window of opportunity to reapply shadows.

Dancer
Lower damage, higher survivability. Evasion bonus, waltzes, and a moderately reliable stun. Also basically the only sub you want if you ever farm Dynamis solo.

Red Mage/Scholar
RDM was the best sub for ninjutsu elemental casting, but the problem is that with the ilevels came few weapons that increased -ton spell damage for it to be remotely worth it (not that it was worth it even before that). I imagine that /RDM can actually survive better than Dancer if you manage your MP correctly given all the tools at your disposal (assuming you don't want something stunned), but it's a lot of work for little payoff; probably better off just playing RDM itself to get the full package. SCH can serve the same sort of function as RDM sub, just with some different mechanics.

Dark Knight, Bard, Beastmaster
If you're returning from a very long time ago you might've seen these subbed on Ninja for their enmity tools. Not really used anymore.

Black Mage
Heck yes, Warps all day long.

Merits

Select your favored Ninja elements and push them to 5/5. Opting for one light aligned element and one dark aligned element will aid you in punching harder on magic bursts on either side of the spectrum.

Your group two options usually begin with 5/5 Sange or close to. The added racc is usually paramount for the purposes behind the job ability. It will help you gain TP, but only if you can land the hits.

Beyond sange, you are free to select your two favored elements in the table again. As you would with the tier 1 merits.

Katanas

When it comes to deciding on which Katana you'd like to use, you are going to need to decide what style of play fits you and your group best. Each of the D.R.E.M.A. weapons have their own particular uses and will often urge you into a specific weaponskill and playstyle.

Heishi Shorinken
Befitting it's visage, it is perhaps the gold standard of Ninja damage dealing as of today. The aeonic weapons, which come from completing the entirety of Gaeas Fete content in Escha, all come with Store TP +10 and TP Bonus +500. If there's anything we've learned from the past with TP Bonus Magian weapons and weapons like the familiar Hagun, it's that TP Bonus can add a lot of damage to weaponskills whose damage multiplication rises quickly in conjuction with TP above 1000. This katana will see you mostly using Blade: Ten as it has incredible fTP scaling. Though you may find yourself straying to Blade: Shun for gaining this weapons aftermath, and other WS's in order to create the Ultimate Skillchain Radiance.

Kikoku
Our tried and true relic. It's gotten Ninjas through many years of clawing their way to being counted among the top DD's in merit parties and end game. While acquiring the base version of this is very quick, you will have many magian trials to complete and fetch quests to let it ascend to it's 119 version. Should you be able to complete the Dynamis Divergence zones and open access to augmenting this weapon, it's augment will increase it's base dmg as well as give it an additional 20% damage on top of the 119's 40% bump to Metsu. Metsu by itself is a weaponskill with great skillchain properties, a good DEX mod, and a fair fTP . When using Metsu with the 119 version, you will also gain a 10% attack bonus. In cases where your acc may be fine, you might wish to throw this weapon into your main slot to make up some of your attack deficiency.

Kannagi
The weapon any Abyssea born Ninja should be familiar with. It gave us access to one of our coolest looking weaponskills. The 119 version's aftermath has also changed from the abyssea era, moving from an Occasionally Deals Double Damage to Occasionally Deals Triple. This weapon serves a lot of damage any time you find your white damage contributing more to your overall damage ratio. Whether you are amnesia'd, holding TP for other party members weaponskills, or just have a seriously inflated crit rate and crit damage you will be very happy with this old friend. You will certainly be using Blade: Hi to enable the 3000 TP aftermath, but after that you may find you'll stray from Hi in order to accommodate other party members skillchains or even your own.

Nagi
Were you looking for Kikoku or Kannagi or Heishi Shorinken?
All jokes aside, while this may have once been an interesting weapon it certainly underperforms as a katana for damage dealing purposes. Tying it's aftermath to a weaponskill that has not aged well definitely hasn't helped this katana at all. Square-Enix has had a history of introducing changes to the Ninja repertoire that seems to see each small niche of this weapon shrink even further. If you were looking for an Enmity Katana, please look at the next one.

Fudo Masamune
Touting unparalleled accuracy, this Katana is crafted using materials found in and outside of the newest Dynamis adventure, Dynamis Divergence. This is a leathercraft synth open only to those leathercrafters who have completed their crafting Escutcheon. This is also the only 'ultimate' katanas that can be bought off of the Auction House should you have the gil. It is an Su5 piece of gear, meaning you will have to be a Job Master Ninja with your stars over your head before you can equip it. Each Divergence weapon is able to be augmented with three different paths. One that mimics an empyrean, one that somewhat mimics a mythics multi-attack, and a third path that will give you access to more enmity than you would have ever found even on the Nagi. This weapon has a lot of flexibility depending on your capacity to acquire the previously mentioned katanas. It can function as a Mainhand katana for you, or as an offhand for a large jump in overall accuracy and white damage.

Shigi
The Shigi is a very convenient and accessible offhand to anyone who has cleared a HTMB or similar tier content. Purchased by trading materials to Oboro in Port Jeuno, it too can be augmented further with more accuracy and DT-. If you're looking for a quick fix to your offhand choices, this is going to be number one on your list due to it's sheer simple availability.

Ochu
Picked up from Sinister Reign, this katana tries it's best to be our empyrean we never had. Best used as an offhand anytime you're looking for more punch on your weaponskills or nuking, this is one of the easiest offhands to acceptably use in almost any scenario. Provided you have the capped augments on the katana, it will outperform most anything else unless they too are sporting their maximum augments. It also gives you a bit of everything from accuracy, ranged accuracy, pure stats, as well as nuking oomph.

Kanaria
If you're feeling particularly lucky, or rather masochistic, you can subject yourself to Oseem and his augment system. This katana comes from Reisenjima Gaeas Fete and is further augmented by Oseem's random system using stones also found from the same zone. This katana can become incredibly powerful as an offhand for nearly any main hand. Or if you're hurting for a main hand it can serve as your mainhand as well. Easy enough to find a few falling to the ground in Reisenjima if a lot of groups are killing NM's. You'll be looking to get augments similar to: DMG18+, DEX8+, Acc/Attk 20+, and Triple Attack 3%.

Malevolence
I would be remiss to not include a few daggers in the list of weapons even though they are not katanas. You will get more mileage out of a couple capped Malevolences than any Katana for nuking Ni and San nukes. Again received from Sinister Reign, like the aforementioned Ochu, at capped augments it will have more Magic Attack Bonus and INT than you'll know what to do with. Dual wield these and nuke the world.

Ternion Dagger +1
If you're looking for a physical focused dagger, you'll find that the Ternion Dagger +1 clocks in at a fairly moderate dmg base with a blazingly fast delay. Accompanied with Triple Attack and added Agility for ranged crit rate, lower tp feed, or a stronger Blade: Hi. You will need to farm a Unity NM for this dagger, but it is one of those items you can get in a single outing depending on your playgroup.

Ambuscade Items

Ambuscade is an event that has brought a lot of accessibility to newly returning players as well as an outlet for veterens to snag some easy loot. There are two gearsets from Ambuscade you will want to look into picking up. Equally important for new players, there is access to a iLvl 119 katana from Ambuscade that will stop-gap you into better things. The penultimate reward of course are the augmentable capes.

Andartia's Mantle
You will find this cape listed in a LOT of sets down below. The ambuscade augment system will give you access to a cape that can be many things. Which do you make first? It's a difficult choice depending on your playstyle and weapon choices, but below are the ones I'd tend to get before any others. You will find some in the gearlists that are not listed here. They could be capes you never make or capes you make first, I'll leave that decision to you.

As stated previously, there are three tiers to the Melee TP gearsets pertaining to availability. These gearsets focus on reducing cycle time as well as rounds-to-ws pushing you to your next WS faster. The gearsets are further broken down into haste recieved sets. You will want to leverage something like a lua script in order to equip these sets automatically based on in-game variables. Or you may wish to find your own solution through the use of EquipSets.

Along with the gearset the specifics for the weaponskill will be given. Use the information to decide if your gearset works for you and your targets. Remember these sets focus mostly on the mod of the weaponskill while taking in little consideration to accuracy or attack needs. I encourage you to discuss your own changes and swaps depending on your attack to defense ratio. Please don't forget to include the ratio (or other environment variables) when bringing a discussion forward about alternates.

Purely magical weaponskills rely heavily on your magic attack bonus. If you find yourself 'cleaving' with a dagger and using Aeolian Edge, or using a katana ws like Blade: Ei or Blade: Yu, focus first on your MAB, then the other supporting stats.

Hybrid weaponskills are a somewhat funky animal. They have two parts to their calculations, the first being a physical damage component. The second being an 'added effect' whose damage is calculated based on a function of the damage done in the physical part. One thing to note is that weaponskill damage is applied in both steps so it's doubly important for us. You may surprise yourself that in the right scenario your hybrid weaponskill might just outperform your other more favorite weaponskill!

Utility gearsets are things you will probably look to build after you've fleshed out your melee TP and chosen weaponskill set. These sets are defensive in nature and can prove to be useful in stemming your premature death in difficult content.

The Andartia's mantle is augmented with DT/PDT/or MDT.
The goal is to substitute a small amount of gear to decrease our damage taken enough to not be a liability to the mages.
In total the suggested changes shown can net you near 47% DT- without sacrificing ~too much~.

I've excluded any Herculean Gear, but do know that they can net DT-4~5%.
Keep in mind that Physical or Magical damage taken for players caps at 50%.
A Shadow Mantle, while not having pdt specifically, will nullify physical damage 6% of the time outside of the -50% Damage Taken cap.

A lot of the most debilitating actions taken against your player can and will be magic based.
Switching to a magic evasion set before being hit with a crippling move or spell is a smart way to give yourself the upper hand.

Should you feel the need to push Ninja's tanking role you will want to find as much Enmity gear as possible.
The options shown at the right are the largest enmity pieces for the time being ignoring Dark Matter Augments.

Casting Gearsets

Casting equipment can get pretty intense. There are a lot of pieces dedicated to casting faster and lowering your interrupts. Do note that you will get 20% casting time reduction from completion of a job point category. This is additive to the fast cast you may already have(need confirmation). Shown below are the precasts and midcasts for the three main types of casting you may end up doing on Ninja.

The stikini rings +1 may be a bit pricey for your taste, but there are other available magic accuracy pieces available. A good example is the Weatherspoon Ring, a questable item.
The Andartia Mantle is augmented with as much magic accuracy as you can cram on it!

When landing Ni or San nukes you will want to push your Magic Attack Bonus while not ignoring your magic accuracy so much as to get resists.
The Herculean Gear shown is expected to have INT/MAB/Macc/Magic Burst Damage.

You may find you need to equip two Ambuscade weapons to gain the large punch you're needing for hitting Omen objectives.
If you are bursting your ninjutsu, there are a few pieces that may aid your damage as shown below.

Two Ambuscade weapons can carry your damage quite a ways.
A Donar Gun will give you Lightning Elemental specific MAB which will multiply your dmg by a separate term!

When bursting, you can use the Samnuha Coat, Locus Ring, Mujin Band, and Hachiya Kyahan +3 to increase your burst dmg.

And don't forget to include your Hattori Tekko when using Futae to multiply your magic damage even further.

Lua/Windower Resources

-To be written.-

Discussion

The more we discuss the more we learn. We should all hope to find the absolute truth in regards to the games idiosyncrasies. I welcome anyone to join in the discussion and bring your ideas and playstyles forward. Please do so without judgement of other players and their playstyles. Keep arguments factual, attack ideas, not people.

DPS Spreadsheet

The DPS spreadsheet is now a community project and maintained by Quetzalcoatl.Langly, credit originally goes to Motenten. Put simply, it does a lot of the already understood math for you instead of you needing to figure out every last bit of minutae. Is it 100% accurate in modeling in game damage output? No, it isn't perfect, but there is a lot of good information to be gleaned from the spreadsheet. Fields like cycle time, base tp rounds, avg weaponskill damage, and average cRatio's can get you a long way in understanding your damage ouput in a vacuum. If there are any issues with the spreadsheets or you have found errors, please make a post and discuss what you believe to be an error. I will move to fix the error as fast as possible.